For basic hierarchical clustering use groups <- hclust(dist(qmu))
But there are many options for function dist() and for function hclust() and these will affect the results. For basic plotting use plot(groups) But as you will see, there are too many cases for the labels to be legible. Hierarchical clustering gives you from 1 to ncases groups. You have to decide where to cut the dendrogram to define a particular number of clusters. Since you are clustering on a single value, you may find kmeans clustering to be more useful You must specify the number of groups in advance, but you can try several group sizes to see what makes the most sense for your data. ---------------------------------------------- David L Carlson Associate Professor of Anthropology Texas A&M University College Station, TX 77843-4352 > -----Original Message----- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of eliza botto > Sent: Monday, July 30, 2012 1:44 AM > To: r-help@r-project.org; smartpink...@yahoo.com > Subject: [R] distance matrix and hclustering > > > Dear R Users,i am very new to R. I want your help on an issue regarding > distance matrix and cluster analysis > i had discharge data of 4 rivers(a,b,c,d) in 4 vectors each having 364 > values > > dput(qmu)structure(list(a = c(0.26, 0.25, 0.25, 0.25, 0.24, 0.23, > 0.22, 0.21, 0.21, 0.21, 0.2, 0.19, 0.19, 0.19, 0.19, 0.18, 0.18, 0.18, > 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, > 0.17, 0.17, 0.17, 0.17, 0.18, 0.19, 0.19, 0.19, 0.2, 0.21, 0.21, 0.21, > 0.21, 0.21, 0.21, 0.19, 0.19, 0.18, 0.17, 0.17, 0.15, 0.18, 0.2, 0.21, > 0.2, 0.19, 0.19, 0.19, 0.2, 0.24, 0.3, 0.3, 0.3, 0.32, 0.34, 0.42, > 0.46, 0.48, 0.67, 0.82, 0.79, 0.73, 0.69, 0.67, 0.67, 0.66, 0.64, 0.61, > 0.58, 0.56, 0.55, 0.55, 0.55, 0.52, 0.49, 0.48, 0.51, 0.53, 0.52, 0.49, > 0.48, 0.48, 0.46, 0.46, 0.44, 0.43, 0.43, 0.41, 0.48, 0.55, 0.57, 0.55, > 0.56, 0.6, 0.64, 0.67, 0.73, 0.84, 0.94, 1.09, 1.24, 1.28, 1.19, 1.11, > 1, 0.92, 0.86, 0.79, 0.76, 0.76, 0.76, 0.76, 0.92, 0.98, 1.03, 1.03, > 1.03, 1.03, 1.07, 1.11, 1.24, 1.44, 2.12, 3.26, 15, 9.45, 5.07, 4.59, > 3.5, 2.84, 2.54, 2.57, 3.01, 2.32, 2.32, 2.97, 2.92, 3.88, 4.76, 5.99, > 3.74, 2.92, 2.65, 2.57, 2.97, 3.4, 4.13, 4.31, 3.89, 3.45, 3.01, 2.88, > 2! > .5, 2.29, 2.39, 2.25, 2.02, 1.87, 1.87, 2.54, 2.69, 2.76, 3.18, 3.74, > 4.59, 4.76, 4.36, 6.56, 5.07, 3.84, 3.55, 3.84, 3.84, 5.49, 5.32, 3.74, > 3.31, 3.4, 3.26, 3.09, 2.69, 2.54, 2.46, 2.39, 2.25, 2.22, 2.22, 2.25, > 2.29, 2.22, 2.18, 2.05, 2.18, 2.39, 2.18, 2.29, 2.11, 1.81, 1.6, 1.44, > 1.41, 1.32, 1.37, 1.37, 1.65, 2.31, 2.25, 1.68, 1.41, 1.26, 1.15, 3.28, > 1.93, 1.6, 1.53, 1.28, 1.13, 1.03, 1.03, 1.03, 1.03, 1, 0.96, 0.92, > 0.87, 0.82, 0.79, 0.76, 0.73, 0.7, 0.67, 0.64, 0.64, 0.61, 0.61, 0.61, > 1.76, 1.19, 1.24, 1.37, 1.68, 2.39, 2.05, 1.78, 1.58, 1.41, 1.39, 1.5, > 1.41, 1.32, 1.19, 1.11, 1.02, 1.07, 4.57, 1.96, 1.68, 1.5, 1.37, 1.24, > 1.11, 1.03, 0.96, 0.94, 2.93, 2.88, 2.92, 2.76, 2.02, 1.71, 1.5, 1.37, > 1.22, 1.09, 1, 0.94, 0.87, 0.81, 0.76, 0.73, 0.7, 0.67, 0.61, 0.58, > 0.57, 0.55, 0.53, 0.51, 0.48, 0.47, 0.44, 0.43, 0.43, 0.41, 0.41, 0.38, > 0.4, 0.4, 0.42, 0.42, 0.41, 0.46, 0.53, 0.55, 0.52, 0.49, 0.51, 0.53, > 0.55, 0.7, 1.03, 1.03, 1.17, 1.24, 1.19, 1.11, 1.03, 0.98, 0.92, 0.84,! > 0.79, 0.75, 0.7, 0.67, 0.61, 0.58, 0.56, 0.56, 0.55, 0.53, 0.51, 0.48 > , 0.46, 0.43, 0.41, 0.38, 0.37, 0.35, 0.34, 0.32, 0.31, 0.3, 0.29, > 0.28, 0.27, 0.25, 0.26, 0.24, 0.23, 0.22, 0.22, 0.21, 0.21, 0.21), b = > c(0.19, 0.19, 0.19, 0.18, 0.18, 0.18, 0.17, 0.17, 0.17, 0.17, 0.16, > 0.17, 0.17, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, > 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.14, 0.14, 0.14, 0.14, 0.14, > 0.14, 0.14, 0.14, 0.14, 0.14, 0.14, 0.14, 0.14, 0.14, 0.14, 0.15, 0.15, > 0.15, 0.15, 0.15, 0.15, 0.15, 0.16, 0.16, 0.17, 0.17, 0.18, 0.18, 0.18, > 0.18, 0.18, 0.18, 0.18, 0.18, 0.19, 0.21, 0.21, 0.21, 0.22, 0.23, 0.24, > 0.24, 0.23, 0.24, 0.24, 0.25, 0.25, 0.25, 0.28, 0.29, 0.29, 0.3, 0.31, > 0.31, 0.34, 0.41, 0.46, 0.51, 0.57, 0.61, 0.64, 0.67, 0.7, 0.76, 0.82, > 0.86, 1.05, 1.24, 1.05, 0.94, 0.92, 0.9, 0.86, 0.82, 0.76, 0.76, 0.76, > 0.78, 0.82, 0.9, 1.07, 1.76, 3.13, 3.64, 3.45, 3.01, 2.39, 2.02, 1.87, > 2.11, 2.02, 1.78, 1.63, 1.53, 1.63, 4.84, 12.5, 8.11, 3.89, 2.73, 2.11, > 1.96, 3.17, 2.65, 2.54, 3.01, 3.31, 3.6, 3.36, 2.76, 2.39, 2.11, 2.! > 25, 2.08, 1.99, 2.11, 2.36, 3.13, 7.16, 5.39, 5.52, 5.32, 4.25, 3.45, > 3.26, 3.18, 3.74, 4.35, 5.79, 5.45, 4.42, 3.84, 3.36, 2.84, 2.39, 3.84, > 3.18, 3.22, 2.97, 2.73, 2.65, 2.92, 4.33, 3.01, 3.01, 3.26, 3.09, 3.6, > 3.64, 4.05, 4.25, 4.48, 3.69, 3.74, 3.6, 3.18, 2.76, 4.11, 2.92, 2.69, > 2.73, 2.69, 3.93, 2.69, 2.18, 2.52, 2.69, 1.99, 2.57, 1.81, 1.55, 1.44, > 1.37, 1.28, 1.19, 1.19, 1.03, 1.03, 1, 0.94, 0.89, 0.87, 0.86, 0.86, > 2.3, 1.55, 1.19, 1.11, 1.5, 1.39, 1.22, 1.24, 1.07, 1.02, 0.96, 0.92, > 1.34, 1.15, 1.03, 2.06, 1.76, 1.3, 1.15, 1.05, 0.98, 0.92, 0.89, 0.84, > 0.81, 0.76, 0.73, 1.59, 5.2, 3.01, 2.05, 1.65, 1.68, 5.29, 2.73, 1.96, > 1.6, 1.41, 1.28, 1.15, 1.11, 1.13, 1.09, 1.03, 6.99, 10.6, 5.39, 3.45, > 2.5, 1.87, 1.68, 1.78, 1.53, 1.41, 1.3, 1.17, 1.05, 0.98, 0.92, 0.9, > 0.87, 0.86, 0.82, 0.78, 0.75, 0.72, 0.67, 0.82, 1.6, 0.89, 0.94, 0.96, > 0.92, 0.87, 0.82, 0.79, 0.75, 0.7, 0.67, 0.64, 0.61, 0.58, 0.56, 0.53, > 0.51, 0.48, 0.47, 0.46, 0.43, 0.41, 0.41, 0.68, 16.3, 17.2, 6.05, 3.6! > 9, 2.92, 2.25, 1.87, 1.63, 1.46, 1.32, 1.19, 1.07, 1, 0.94, 0.89, 0.87 > , 0.86, 0.81, 0.76, 0.73, 0.7, 0.7, 0.7, 0.7, 0.7, 0.67, 0.67, 0.66, > 0.64, 0.61, 0.58, 0.56, 0.55, 0.53, 0.51, 0.48, 0.46, 0.44, 0.43, 0.43, > 0.41, 0.4, 0.38, 0.37, 0.36, 0.35, 0.34, 0.33, 0.32, 0.31, 0.31, 0.3, > 0.3, 0.29, 0.29, 0.28, 0.27, 0.27), c = c(0.27, 0.25, 0.25, 0.25, 0.24, > 0.24, 0.23, 0.22, 0.22, 0.21, 0.21, 0.21, 0.21, 0.21, 0.2, 0.19, 0.19, > 0.19, 0.19, 0.19, 0.19, 0.19, 0.19, 0.19, 0.19, 0.19, 0.19, 0.19, 0.19, > 0.18, 0.18, 0.18, 0.18, 0.18, 0.18, 0.18, 0.18, 0.18, 0.18, 0.17, 0.17, > 0.17, 0.16, 0.15, 0.15, 0.15, 0.14, 0.14, 0.14, 0.14, 0.13, 0.13, 0.13, > 0.13, 0.13, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, > 0.12, 0.13, 0.14, 0.15, 0.15, 0.16, 0.17, 0.18, 0.2, 0.21, 0.23, 0.25, > 0.27, 0.29, 0.31, 0.32, 0.31, 0.32, 0.32, 0.32, 0.32, 0.32, 0.32, 0.32, > 0.32, 0.32, 0.32, 0.32, 0.3, 0.28, 0.28, 0.3, 0.33, 0.35, 0.4, 0.43, > 0.47, 0.52, 0.52, 0.51, 0.53, 0.56, 0.58, 0.58, 0.55, 0.51, 0.47, 0.47, > 0.47, 0.46, 0.48, 0.51, 0.56, 0.61, 0.73, 1, 1.34, 1.73, 8.71, ! > 9.98, 11.1, 5.92, 3.8, 2.84, 2.69, 3.35, 3.89, 4.8, 5.79, 5.2, 4.36, > 3.69, 3.5, 2.92, 2.5, 2.32, 2.65, 2.92, 2.8, 3.94, 5.39, 3.55, 2.92, > 4.65, 6.15, 4.03, 2.88, 2.39, 2.08, 1.93, 1.81, 1.55, 1.34, 1.44, 2.29, > 2.92, 2.92, 2.73, 2.57, 2.73, 3.01, 3.18, 3.09, 6.32, 10.9, 4.25, 3.22, > 2.92, 7.77, 20.8, 6.27, 3.84, 3.01, 2.69, 2.39, 2.32, 2.32, 2.32, 2.15, > 2.32, 2.32, 2.57, 3.15, 2.61, 2.05, 1.76, 1.53, 1.65, 1.71, 1.73, 1.63, > 1.76, 1.87, 1.9, 1.84, 1.81, 1.84, 1.73, 2.08, 1.65, 1.58, 1.5, 1.41, > 1.37, 1.28, 1.32, 1.19, 1.05, 1.09, 1.09, 1, 0.98, 0.94, 0.92, 0.9, > 0.87, 0.86, 0.82, 0.79, 0.79, 0.79, 1.09, 1.05, 1.05, 1.03, 0.96, 0.9, > 0.82, 0.79, 0.76, 0.76, 0.73, 0.72, 0.67, 0.63, 0.58, 0.57, 0.55, 0.52, > 0.51, 0.51, 0.49, 0.48, 0.49, 0.49, 0.51, 0.51, 0.51, 0.51, 0.51, 0.51, > 1.33, 0.92, 0.76, 0.76, 1.16, 1.39, 1.34, 1.26, 1.17, 1.07, 1, 0.92, > 0.86, 0.81, 0.76, 0.72, 0.67, 0.64, 0.61, 0.58, 0.56, 0.53, 0.51, 0.49, > 0.48, 0.46, 0.43, 0.43, 0.43, 0.42, 0.41, 0.38, 0.36, 0.34, 0.32, 0.! > 32, 0.32, 0.31, 0.31, 0.29, 0.28, 0.28, 0.27, 0.27, 0.27, 0.26, 0.26, > 0.25, 0.26, 0.25, 0.25, 0.24, 0.23, 0.22, 0.21, 0.19, 0.19, 0.19, 0.18, > 0.18, 0.21, 0.4, 0.41, 0.43, 0.43, 0.43, 0.44, 0.46, 0.49, 0.51, 0.51, > 0.55, 0.56, 0.53, 0.51, 0.48, 0.46, 0.42, 0.41, 0.41, 0.38, 0.35, 0.36, > 0.34, 0.34, 0.32, 0.31, 0.29, 0.27, 0.26, 0.24, 0.24, 0.21, 0.19, 0.19, > 0.18, 0.18, 0.18, 0.17, 0.16, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.14, > 0.14), d = c(0.13, 0.13, 0.13, 0.13, 0.12, 0.12, 0.13, 0.13, 0.12, > 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, > 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.13, > 0.13, 0.13, 0.16, 0.2, 0.19, 0.17, 0.17, 0.16, 0.16, 0.16, 0.16, > 0.18, 0.17, 0.16, 0.16, 0.16, 0.16, 0.15, 0.15, 0.14, 0.13, 0.13, > 0.16, 0.15, 0.15, 0.14, 0.14, 0.14, 0.14, 0.14, 0.14, 0.14, 0.14, > 0.14, 0.14, 0.13, 0.13, 0.13, 0.12, 0.12, 0.12, 0.12, 0.11, 0.12, > 0.13, 0.14, 0.16, 0.16, 0.17, 0.23, 0.28, 0.28, 0.31, 0.32, 0.37, > 0.41, 0.37, 0.36, 0.34, 0.39, 0.4, 0.37, 0.34, 0.33, 0.32, 0.2! > 9, 0.28, 0.28, 0.28, 0.28, 0.28, 0.26, 0.27, 0.28, 0.28, 0.36, > 0.52, 0.63, 1.12, 1.02, 1.19, 1.51, 1.72, 1.97, 3.11, 2.77, 2.19, > 1.86, 1.62, 1.39, 1.16, 1.04, 0.96, 0.91, 0.9, 0.93, 1.21, 1.31, > 1.46, 1.59, 1.46, 1.49, 1.54, 1.62, 1.83, 2.14, 2.22, 2.16, 2.14, > 2.33, 2.47, 2.14, 1.97, 2, 2.53, 2.81, 2.85, 2.81, 2.92, 3, 3.21, > 3.43, 3.3, 3.17, 2.4, 2.02, 2.66, 3.56, 8.31, 5.92, 5.99, 5.92, > 4.93, 4.98, 5.19, 4.41, 5.57, 4.87, 4.04, 3.79, 3.61, 3.89, 3.7, > 3.66, 3.7, 3.89, 4.47, 7.77, 5.44, 3.89, 3.17, 2.92, 2.62, 2.26, > 2.14, 2.16, 2.14, 2.16, 2.11, 1.97, 1.89, 1.83, 1.86, 1.97, 1.83, > 1.57, 1.29, 1.14, 1.04, 0.98, 1, 0.98, 0.96, 1, 1.39, 1.21, 1.1, > 1.04, 0.98, 0.94, 0.93, 0.93, 0.93, 0.9, 0.9, 0.9, 0.88, 0.86, > 0.83, 0.83, 0.83, 0.8, 0.78, 0.74, 0.69, 0.64, 0.61, 0.6, 0.61, > 0.6, 1.99, 2.3, 1.54, 1.54, 1.44, 1.29, 1.14, 1.04, 0.96, 0.96, > 1.08, 1.1, 1.08, 1.02, 0.94, 0.91, 0.86, 0.8, 0.77, 0.7, 0.64, > 0.61, 3.28, 1.62, 1! > .64, 1.49, 1.39, 1.29, 1.14, 1.04, 0.96, 0.9, 0.85, 0.78, 0.74, 0. > 7, 0.67, 0.63, 0.58, 0.55, 0.52, 0.51, 0.49, 0.48, 0.45, 0.44, > 0.43, 0.41, 0.4, 1.29, 11.6, 14, 4.68, 2.92, 2.19, 1.78, 1.54, > 1.41, 1.29, 1.14, 1.04, 0.98, 0.94, 0.9, 0.83, 0.78, 0.74, 0.67, > 0.64, 0.61, 0.58, 0.55, 0.51, 0.46, 0.46, 0.45, 0.44, 0.44, 0.43, > 0.41, 0.4, 0.39, 0.39, 0.39, 0.39, 0.36, 0.36, 0.36, 0.36, 0.36, > 0.35, 0.35, 0.35, 0.34, 0.36, 0.35, 0.34, 0.34, 0.34, 0.34, 0.34, > 0.34, 0.35, 0.35, 0.36, 0.36, 0.37, 0.36, 0.36, 0.35, 0.34, 0.34, > 0.32, 0.32, 0.32, 0.31, 0.31, 0.31, 0.31, 0.31, 0.31, 0.29, 0.28, > 0.26, 0.25, 0.24, 0.22, 0.2, 0.19, 0.18, 0.17, 0.16, 0.15)), .Names > = c("a", "b", "c", "d"), class = "data.frame", row.names = c(NA, - > 364L)) > > by using "as.matrix", i converted by data into a matrix. Now, I want to > create a distance matrix. My data as shown above contains 364 rows and > 4 columns. I have to create distance matrix based on the values of 2nd > column. > secondly, based on this distance matrix i would like to do > "hclustering", to see which of the rivers have similar discharge > patterns. more precisely, i need to see river(a,b,c,d) splitted in > clusters with river having similar discharge patterns in one cluster. > thnx in advanceeliza botto > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.